SAXSdb — 3da7

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Barstar

Bacillus amyloliquefaciens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Barnase circular permutant × 1 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Barnase circular permutant × 1 water × 2	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 2	Barnase circular permutant × 1 water × 2	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 2	Barnase circular permutant × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	BARS_BACAM
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 1–90； UniProt 1–90 Author chain D； PDBConstruct 1–90； UniProt 1–90 Author chain F； PDBConstruct 1–90； UniProt 1–90 Author chain H； PDBConstruct 1–90； UniProt 1–90

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	3da7
Deposition date deposition_date	2008-05-28
Structure title title	A conformationally strained, circular permutant of barnase
Keywords keywords	CIRCULAR PERMUTANT, PROTEIN-PROTEIN COMPLEX, ENDONUCLEASE, Cytoplasm, PROTEIN BINDING; PROTEIN BINDING
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

3da7__assembly_3__model_1

Assembly 3 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

3da7__assembly_3__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3da7__assembly_3__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	17.98 Å
Rg (electron density)	17.12 Å
Total Rg	18.09 Å
Atom count	1549
Residues	193
Excluded volume	27443 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3da7__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3da7__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`3da7__assembly_3__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`3da7__assembly_4__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Barnase circular permutant
Molecular weight formula_weight	12501.9 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,E,G
Atom count atom_count	6544

SGRTWREADINYTSGFRNSDRILYSSDWLIYKTTDHYQTFTKIRCAQVINTFDGVADYLQTYHKLPDNYITKSEAQALGWVASKGNLADVAPGKSIGGDIFSNREGKLPGK

Source Source

Source organism organism	Bacillus amyloliquefaciens
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Barstar
Molecular weight formula_weight	10352.7 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,D,F,H

MKKAVINGEQIRSISDLHQTLKKELALPEYYGENLDALWDCLTGWVEYPLVLEWRQFEQSKQLTENGAESVLQVFREAKAEGCDITIILS

Source Source

Source organism organism	Bacillus amyloliquefaciens
NCBI taxonomy ID ncbi_taxonomy_id	1390
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	372

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6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d3da7c_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.9 — Barstar-like
Superfamily Superfamily superfamily	c.9.1 — Barstar-related
Family Family family	c.9.1.1 — Barstar-related

Domain ID domain_id	d3da7d_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.9 — Barstar-like
Superfamily Superfamily superfamily	c.9.1 — Barstar-related
Family Family family	c.9.1.1 — Barstar-related

Domain ID domain_id	d3da7f_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.9 — Barstar-like
Superfamily Superfamily superfamily	c.9.1 — Barstar-related
Family Family family	c.9.1.1 — Barstar-related

Domain ID domain_id	d3da7h_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.9 — Barstar-like
Superfamily Superfamily superfamily	c.9.1 — Barstar-related
Family Family family	c.9.1.1 — Barstar-related

CATH v4.4 (8 domains)

Domain ID domain_id	3da7A00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	20 — Severin
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	3da7B00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	20 — Severin
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	3da7C00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	370 — Barnase; Chain D
Homologous superfamily homologous superfamily	10 — Barstar-like

Domain ID domain_id	3da7D00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	370 — Barnase; Chain D
Homologous superfamily homologous superfamily	10 — Barstar-like

Domain ID domain_id	3da7E00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	20 — Severin
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	3da7F00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	370 — Barnase; Chain D
Homologous superfamily homologous superfamily	10 — Barstar-like

Domain ID domain_id	3da7G00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	20 — Severin
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	3da7H00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	370 — Barnase; Chain D
Homologous superfamily homologous superfamily	10 — Barstar-like

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Unit-cell length a length_a	38.879 Å
Unit-cell length b length_b	80.237 Å
Unit-cell length c length_c	81.922 Å
Unit-cell angle α angle_alpha	88.10 °
Unit-cell angle β angle_beta	76.98 °
Unit-cell angle γ angle_gamma	79.47 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	2.250 Å
Low-resolution limit resolution_low	19.870 Å
R factor r_factor	0.2070
R_work r_work	0.2050
R_free r_free	0.2500

A conformationally strained, circular permutant of barnase

1. Protein Identity and Related Structures Protein Identity & Related Structures

Barstar

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

3da7__assembly_3__model_1

3da7__assembly_3__model_1 | I(q)

3da7__assembly_3__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (4 domains)

CATH v4.4 (8 domains)

7. Citations (1)

A conformationally strained, circular permutant of barnase

1. Protein Identity and Related Structures Protein Identity & Related Structures

Barstar

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

3da7__assembly_3__model_1

3da7__assembly_3__model_1 | I(q)

3da7__assembly_3__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (4 domains)

CATH v4.4 (8 domains)

7. Citations (1)